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Goal

Enacting Taverna workflows through Galaxy

Introduction

The diversity and availability of bioinformatics tools have increased in recent years. Some tools deal with the same problem using a different approach, others provide different access mechanisms to the same resources while others provide aggregation mechanisms to make use of a number of tools in a uniform way. For the latter, software pipelining systems, are becoming the norm in bioinformatics. Widely used examples of such systems are Galaxy, a web-portal and framework, and Taverna, a workflow management system. The goal of both of these systems is to provide a platform that bioinformaticians and biologists can use to describe their experiments in a number of well described processing steps, i.e. workflows.

However, the approach used is different. In Galaxy the focus is on an intuitive and easy to use user interface, a web-based portal, to aggregate several bioinformatics tools and expose them in a uniform way. Taverna is a workflow management system that allows for the orchestration of a wide range of services. It provides good extensibility points to add new functionality using a plug-in framework. It offers a powerful and flexible workflow language that allows for the description of complex workflows that include repetitions, conditionals and other well understood programming language constructs.

Both of the above mentioned systems provide a wide range of functionality out of the box. There is some overlap but the real added value would be if we could combine that functionality and try to get the best of both systems. This work aims to bridge the two by allowing the more expressive but complex Taverna workflows to execute via the simple and intuitive interface that Galaxy offers. To this end we built a Galaxy tool generator that given a Taverna workflow description and a Taverna Server it constructs a Galaxy tool to enable the enactment of that workflow via Galaxy.

The generator provides a command-line interface (workflow_to_galaxy.rb) that can create a Galaxy tool from either a t2flow workflow file or via a URL of a workflow as exposed by the myExperiment workflow repository (www.myexperiment.org). For convenience the generator is also available in myExperiment, and it will generate the Galaxy tool behind the scenes. The bioinformatician will just browse the myExperiment repository to identify Taverna workflows that are of interest to him/her and he will be able to download them as Galaxy tools which can then be installed into a Galaxy server in the usual way.

There are plans to further automate this procedure by accessing the myExperiment site as a Galaxy external interface, which will dynamically add the workflows as new tools in Galaxy.

Installation and Requirements

The tool is implemented in Ruby, so a Ruby development environment needs to be available. Native packages of libxml, libopenssl and zlib may be required. Please use your favorite package manager to install them (an apt-get example is given). Note that some of the following native packages might already be installed in your system. For Debian-based systems, use this command:

Attachments

myexperiment-rest-0.2.5.gem
(19.5 KB) - added by kostas.karasavvas@…4 years ago.
Given a myExperiment URL of a Taverna2 workflow it provides a workflow object with everything needed to generate the Galaxy tool. Uses myExperiments REST API. Also contains the Taverna workflow classes to be used without myExperiment.